Bottom Line:
The best fit, however, is obtained with NBDM regimes lacking strand effects, which indicates that over the long term NBDM switches strands in the germline as one would expect for effects due to loosely contained background transcription.We conclude that the primary structure of vertebrate genic DNA at and below the trinucleotide level has been governed over the long term by highly conserved regimes of NBDM which should be under direct natural selection because they alter drastically missense-mutation rates and hence the somatic and the germline mutational loads.Therefore, the non-coding DNA of vertebrates may have been shaped by NBDM only epiphenomenally, with non-genic DNA being affected mainly when found in the proximity of genes.

Affiliation: Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America. marcos.antezana@gmail.com

ABSTRACTThe content of guanine+cytosine varies markedly along the chromosomes of homeotherms and great effort has been devoted to studying this heterogeneity and its biological implications. Already before the DNA-sequencing era, however, it was established that the dinucleotides in the DNA of mammals in particular, and of most organisms in general, show striking over- and under-representations that cannot be explained by the base composition. Here we show that in the coding regions of vertebrates both GC content and codon occurrences are strongly correlated with such "motif preferences" even though we quantify the latter using an index that is not affected by the base composition, codon usage, and protein-sequence encoding. These correlations are likely to be the result of the long-term shaping of the primary structure of genic and non-genic DNA by a regime of mutation of which central features have been maintained by natural selection. We find indeed that these preferences are conserved in vertebrates even more rigidly than codon occurrences and we show that the occurrence-preference correlations are stronger in intronic and non-genic DNA, with the R(2)s reaching 99% when GC content is approximately 0.5. The mutation regime appears to be characterized by rates that depend markedly on the bases present at the site preceding and at that following each mutating site, because when we estimate such rates of neighbor-base-dependent mutation (NBDM) from substitutions retrieved from alignments of coding, intronic, and non-genic mammalian DNA sorted and grouped by GC content, they suffice to simulate DNA sequences in which motif occurrences and preferences as well as the correlations of motif preferences with GC content and with motif occurrences, are very similar to the mammalian ones. The best fit, however, is obtained with NBDM regimes lacking strand effects, which indicates that over the long term NBDM switches strands in the germline as one would expect for effects due to loosely contained background transcription. Finally, we show that human coding regions are less mutable under the estimated NBDM regimes than under matched context-independent mutation and that this entails marked differences between the spectra of amino-acid mutations that either mutation regime should generate. In the Discussion we examine the mechanisms likely to underlie NBDM heterogeneity along chromosomes and propose that it reflects how the diversity and activity of lesion-bypass polymerases (LBPs) track the landscapes of scheduled and non-scheduled genome repair, replication, and transcription during the cell cycle. We conclude that the primary structure of vertebrate genic DNA at and below the trinucleotide level has been governed over the long term by highly conserved regimes of NBDM which should be under direct natural selection because they alter drastically missense-mutation rates and hence the somatic and the germline mutational loads. Therefore, the non-coding DNA of vertebrates may have been shaped by NBDM only epiphenomenally, with non-genic DNA being affected mainly when found in the proximity of genes.

pone-0002145-g016: Transcribed-strand asymmetries of the occurrences and preferences of complementary 3/1 dinucleotides as a function of GC3.For each GC-sorted gene group, the asymmetries within each of the six pairs of non-identical complementary dinucleotides are expressed as the signed difference (delta) between the values of pair members. Clockwise from the top left: deltas for occurrence frequencies, for 1-composition expectations, for motif preferences, and for the difference between observed and expected occurrence deltas. In all plots pairs are labelled as in the upper right plot (where ct-ag hides tc-ga, however).

Mentions:
The sum within each GC-sorted gene group of the absolute values of the differences (deltas) between values for complementary bases, 3/1 dinucleotides, and trinucleotides (top, middle, and bottom). At the top left are overall base-occurrence asymmetries at each codon position and on the right the TvsA and CvsG individual deltas. Also shown are base-composition predictions for all genes and asymmetries in 90 ribosomal-protein genes (subdivided into 6 groups, white signs, left plot only). In the middle and bottom are occurrence asymmetries and motif-preference asymmetries (left, right), for 3/1 dinucleotides and for codons or across-codon trinucleotides (see also Figure 16 and 17 for individual-motif deltas). Grey lines on the left are the base-composition expectations and on the right the “” asymmetries of motif preferences from genes with previously randomized synonymous-codon locations. The +signs are for ribosomal-protein genes and the white +'s are the base-composition predictions.

pone-0002145-g016: Transcribed-strand asymmetries of the occurrences and preferences of complementary 3/1 dinucleotides as a function of GC3.For each GC-sorted gene group, the asymmetries within each of the six pairs of non-identical complementary dinucleotides are expressed as the signed difference (delta) between the values of pair members. Clockwise from the top left: deltas for occurrence frequencies, for 1-composition expectations, for motif preferences, and for the difference between observed and expected occurrence deltas. In all plots pairs are labelled as in the upper right plot (where ct-ag hides tc-ga, however).

Mentions:
The sum within each GC-sorted gene group of the absolute values of the differences (deltas) between values for complementary bases, 3/1 dinucleotides, and trinucleotides (top, middle, and bottom). At the top left are overall base-occurrence asymmetries at each codon position and on the right the TvsA and CvsG individual deltas. Also shown are base-composition predictions for all genes and asymmetries in 90 ribosomal-protein genes (subdivided into 6 groups, white signs, left plot only). In the middle and bottom are occurrence asymmetries and motif-preference asymmetries (left, right), for 3/1 dinucleotides and for codons or across-codon trinucleotides (see also Figure 16 and 17 for individual-motif deltas). Grey lines on the left are the base-composition expectations and on the right the “” asymmetries of motif preferences from genes with previously randomized synonymous-codon locations. The +signs are for ribosomal-protein genes and the white +'s are the base-composition predictions.

Bottom Line:
The best fit, however, is obtained with NBDM regimes lacking strand effects, which indicates that over the long term NBDM switches strands in the germline as one would expect for effects due to loosely contained background transcription.We conclude that the primary structure of vertebrate genic DNA at and below the trinucleotide level has been governed over the long term by highly conserved regimes of NBDM which should be under direct natural selection because they alter drastically missense-mutation rates and hence the somatic and the germline mutational loads.Therefore, the non-coding DNA of vertebrates may have been shaped by NBDM only epiphenomenally, with non-genic DNA being affected mainly when found in the proximity of genes.

Affiliation:
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America. marcos.antezana@gmail.com

ABSTRACTThe content of guanine+cytosine varies markedly along the chromosomes of homeotherms and great effort has been devoted to studying this heterogeneity and its biological implications. Already before the DNA-sequencing era, however, it was established that the dinucleotides in the DNA of mammals in particular, and of most organisms in general, show striking over- and under-representations that cannot be explained by the base composition. Here we show that in the coding regions of vertebrates both GC content and codon occurrences are strongly correlated with such "motif preferences" even though we quantify the latter using an index that is not affected by the base composition, codon usage, and protein-sequence encoding. These correlations are likely to be the result of the long-term shaping of the primary structure of genic and non-genic DNA by a regime of mutation of which central features have been maintained by natural selection. We find indeed that these preferences are conserved in vertebrates even more rigidly than codon occurrences and we show that the occurrence-preference correlations are stronger in intronic and non-genic DNA, with the R(2)s reaching 99% when GC content is approximately 0.5. The mutation regime appears to be characterized by rates that depend markedly on the bases present at the site preceding and at that following each mutating site, because when we estimate such rates of neighbor-base-dependent mutation (NBDM) from substitutions retrieved from alignments of coding, intronic, and non-genic mammalian DNA sorted and grouped by GC content, they suffice to simulate DNA sequences in which motif occurrences and preferences as well as the correlations of motif preferences with GC content and with motif occurrences, are very similar to the mammalian ones. The best fit, however, is obtained with NBDM regimes lacking strand effects, which indicates that over the long term NBDM switches strands in the germline as one would expect for effects due to loosely contained background transcription. Finally, we show that human coding regions are less mutable under the estimated NBDM regimes than under matched context-independent mutation and that this entails marked differences between the spectra of amino-acid mutations that either mutation regime should generate. In the Discussion we examine the mechanisms likely to underlie NBDM heterogeneity along chromosomes and propose that it reflects how the diversity and activity of lesion-bypass polymerases (LBPs) track the landscapes of scheduled and non-scheduled genome repair, replication, and transcription during the cell cycle. We conclude that the primary structure of vertebrate genic DNA at and below the trinucleotide level has been governed over the long term by highly conserved regimes of NBDM which should be under direct natural selection because they alter drastically missense-mutation rates and hence the somatic and the germline mutational loads. Therefore, the non-coding DNA of vertebrates may have been shaped by NBDM only epiphenomenally, with non-genic DNA being affected mainly when found in the proximity of genes.